rs10813923

Variant names:

• chr9-33023519-G-A
• rs10813923
• ENST00000468275.6:c.-5+1285C>T

Your query was ambiguous. Multiple possible variants found:

• chr9-33023519-G-A
• chr9-33023519-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000468275.6(APTX):​c.-5+1285C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.124 in 152,258 control chromosomes in the GnomAD database, including 1,312 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.12 (1312 hom., cov: 33)
• Consequence: APTX ENST00000468275.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.627
• Publications: 1 publications found

Genes affected

APTX (HGNC:15984): (aprataxin) This gene encodes a member of the histidine triad (HIT) superfamily. The encoded protein may play a role in single-stranded DNA repair through its nucleotide-binding activity and its diadenosine polyphosphate hydrolase activity. Mutations in this gene have been associated with ataxia-ocular apraxia. Alternatively spliced transcript variants have been identified for this gene.[provided by RefSeq, Aug 2010]

APTX Gene-Disease associations (from GenCC):

• ataxia, early-onset, with oculomotor apraxia and hypoalbuminemia

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), G2P, Genomics England PanelApp

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000468275.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	APTX	NM_001368995.1		c.-5+1481C>T		intron	N/A	NP_001355924.1
	APTX	NM_001368996.1		c.-5+1504C>T		intron	N/A	NP_001355925.1
	APTX	NM_001368997.1		c.-5+1285C>T		intron	N/A	NP_001355926.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	APTX	ENST00000468275.6	TSL:1	c.-5+1285C>T		intron	N/A	ENSP00000420263.2
	APTX	ENST00000436040.7	TSL:1	c.-5+1504C>T		intron	N/A	ENSP00000400806.4
	APTX	ENST00000460940.6	TSL:1	n.-5+1481C>T		intron	N/A	ENSP00000418311.1

Frequencies

GnomAD3 genomes AF: 0.124 AC: 18812 AN: 152140 Hom.: 1311 Cov.: 33

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0827

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.169

Gnomad FIN AF: 0.0704

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.102

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.124 AC: 18823 AN: 152258 Hom.: 1312 Cov.: 33 AF XY: 0.124 AC XY: 9261 AN XY: 74452

African (AFR) AF: 0.157 AC: 6523 AN: 41530

American (AMR) AF: 0.0825 AC: 1263 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.103 AC: 356 AN: 3472

East Asian (EAS) AF: 0.285 AC: 1473 AN: 5176

South Asian (SAS) AF: 0.170 AC: 821 AN: 4828

European-Finnish (FIN) AF: 0.0704 AC: 747 AN: 10610

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7369 AN: 68020

Other (OTH) AF: 0.101 AC: 213 AN: 2116

Alfa AF: 0.113 Hom.: 511

Bravo AF: 0.123

Asia WGS AF: 0.175 AC: 609 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.74
PhyloP100		-0.63

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10813923; hg19: chr9-33023517;